From nassar at renci.org Thu Nov 2 14:57:32 2006 From: nassar at renci.org (Nassib Nassar) Date: Thu, 2 Nov 2006 14:57:32 -0500 Subject: [MOBY-l] MOBY tutorial - Taverna Message-ID: <20061102195731.GA2080@renci.org> (Thanks to Paul for the test client fix.) I'm having trouble using the ConvertAAtoFASTA_AA servlet example from within Taverna. I made a simple workflow to test this, and everything works perfectly if I send the biomoby service a fully formed XML input but not if I build the input using biomoby processor objects. The workflow runs both cases in parallel: Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml Inputs: http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml Error detail: http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml The error is "Task failed due to problem invoking biomoby service. / SAXParseException: Premature end of file." Tomcat's log reports non-XML in the SOAP message (and it actually appears to be non-ASCII). I also see differences in the input XML constructed by the AminoAcidSequence object, such as missing articleName='inseq' in element moby:Simple. I've tried this with the Taverna 1.4 release, the stable snapshot from October 2, and recent builds from cvs (hopefully including the newer biomoby plug-in module), and it seems I get the same results in all cases. Maybe I'm building the input objects incorrectly? Nassib From nassar at renci.org Thu Nov 2 16:06:22 2006 From: nassar at renci.org ('Nassib Nassar') Date: Thu, 2 Nov 2006 16:06:22 -0500 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <006401c6febc$b22454b0$6900a8c0@notebook> References: <20061102195731.GA2080@renci.org> <006401c6febc$b22454b0$6900a8c0@notebook> Message-ID: <20061102210622.GA2691@renci.org> Hi Eddie, Thanks. Note that if you simulate this problem by setting in the sample XML input (in_test), it generates a very different kind of error - Taverna reports that the process completed (not failed) and returns a MOBY object containing an exception: java.lang.IllegalArgumentException: While executing service: required primary value "inseq" in job 1 is missing So while that is a problem, the error I'm getting is different and appears to be an even more basic problem. Nassib On Thu, Nov 02, 2006 at 12:23:00PM -0800, Edward Kawas wrote: > Hi Nassar, > > It seems that the articlename for the input isnt being set. I will look into > this further. > > Thanks, > > Eddie > > > -----Original Message----- > > From: moby-l-bounces at lists.open-bio.org > > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Nassib Nassar > > Sent: Thursday, November 02, 2006 11:58 AM > > To: moby-l at lists.open-bio.org > > Subject: [MOBY-l] MOBY tutorial - Taverna > > > > (Thanks to Paul for the test client fix.) > > > > I'm having trouble using the ConvertAAtoFASTA_AA servlet > > example from within Taverna. I made a simple workflow to > > test this, and everything works perfectly if I send the > > biomoby service a fully formed XML input but not if I build > > the input using biomoby processor objects. The workflow runs > > both cases in parallel: > > > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > > Inputs: > > http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > > Error detail: > > http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > > > The error is "Task failed due to problem invoking biomoby service. / > > SAXParseException: Premature end of file." Tomcat's log > > reports non-XML in the SOAP message (and it actually appears > > to be non-ASCII). > > I also see differences in the input XML constructed by the > > AminoAcidSequence object, such as missing articleName='inseq' > > in element moby:Simple. > > > > I've tried this with the Taverna 1.4 release, the stable > > snapshot from October 2, and recent builds from cvs > > (hopefully including the newer biomoby plug-in module), and > > it seems I get the same results in all cases. > > > > Maybe I'm building the input objects incorrectly? > > > > Nassib > > _______________________________________________ > > moby-l mailing list > > moby-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-l From nassar at renci.org Thu Nov 2 16:08:26 2006 From: nassar at renci.org ('Nassib Nassar') Date: Thu, 2 Nov 2006 16:08:26 -0500 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <007801c6fec1$7ac40dd0$6900a8c0@notebook> References: <20061102195731.GA2080@renci.org> <007801c6fec1$7ac40dd0$6900a8c0@notebook> Message-ID: <20061102210826.GA2736@renci.org> I followed the tutorial at: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/deployingServices.html Nassib On Thu, Nov 02, 2006 at 12:57:14PM -0800, Edward Kawas wrote: > Sorry about the previous message. I was 'misread' the workflow. The articlenames > are set correctly. So I don't know why one works over the other. > > How did you generate the service provider code? > > Eddie > > > -----Original Message----- > > From: moby-l-bounces at lists.open-bio.org > > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Nassib Nassar > > Sent: Thursday, November 02, 2006 11:58 AM > > To: moby-l at lists.open-bio.org > > Subject: [MOBY-l] MOBY tutorial - Taverna > > > > (Thanks to Paul for the test client fix.) > > > > I'm having trouble using the ConvertAAtoFASTA_AA servlet > > example from within Taverna. I made a simple workflow to > > test this, and everything works perfectly if I send the > > biomoby service a fully formed XML input but not if I build > > the input using biomoby processor objects. The workflow runs > > both cases in parallel: > > > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > > Inputs: > > http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > > Error detail: > > http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > > > The error is "Task failed due to problem invoking biomoby service. / > > SAXParseException: Premature end of file." Tomcat's log > > reports non-XML in the SOAP message (and it actually appears > > to be non-ASCII). > > I also see differences in the input XML constructed by the > > AminoAcidSequence object, such as missing articleName='inseq' > > in element moby:Simple. > > > > I've tried this with the Taverna 1.4 release, the stable > > snapshot from October 2, and recent builds from cvs > > (hopefully including the newer biomoby plug-in module), and > > it seems I get the same results in all cases. > > > > Maybe I'm building the input objects incorrectly? > > > > Nassib > > _______________________________________________ > > moby-l mailing list > > moby-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-l From edward.kawas at gmail.com Thu Nov 2 15:57:14 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Nov 2006 12:57:14 -0800 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <20061102195731.GA2080@renci.org> Message-ID: <007801c6fec1$7ac40dd0$6900a8c0@notebook> Sorry about the previous message. I was 'misread' the workflow. The articlenames are set correctly. So I don't know why one works over the other. How did you generate the service provider code? Eddie > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Nassib Nassar > Sent: Thursday, November 02, 2006 11:58 AM > To: moby-l at lists.open-bio.org > Subject: [MOBY-l] MOBY tutorial - Taverna > > (Thanks to Paul for the test client fix.) > > I'm having trouble using the ConvertAAtoFASTA_AA servlet > example from within Taverna. I made a simple workflow to > test this, and everything works perfectly if I send the > biomoby service a fully formed XML input but not if I build > the input using biomoby processor objects. The workflow runs > both cases in parallel: > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > Inputs: > http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > Error detail: > http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > The error is "Task failed due to problem invoking biomoby service. / > SAXParseException: Premature end of file." Tomcat's log > reports non-XML in the SOAP message (and it actually appears > to be non-ASCII). > I also see differences in the input XML constructed by the > AminoAcidSequence object, such as missing articleName='inseq' > in element moby:Simple. > > I've tried this with the Taverna 1.4 release, the stable > snapshot from October 2, and recent builds from cvs > (hopefully including the newer biomoby plug-in module), and > it seems I get the same results in all cases. > > Maybe I'm building the input objects incorrectly? > > Nassib > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From gordonp at ucalgary.ca Thu Nov 2 16:52:34 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 02 Nov 2006 14:52:34 -0700 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <20061102195731.GA2080@renci.org> References: <20061102195731.GA2080@renci.org> Message-ID: <454A68A2.2040705@ucalgary.ca> Hi Nassib, If you could send the Tomcat error, I might have a better idea of the issue. Regards, Paul > (Thanks to Paul for the test client fix.) > > I'm having trouble using the ConvertAAtoFASTA_AA servlet example from > within Taverna. I made a simple workflow to test this, and everything > works perfectly if I send the biomoby service a fully formed XML input > but not if I build the input using biomoby processor objects. The > workflow runs both cases in parallel: > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > Inputs: http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > Error detail: http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > The error is "Task failed due to problem invoking biomoby service. / > SAXParseException: Premature end of file." Tomcat's log reports > non-XML in the SOAP message (and it actually appears to be non-ASCII). > I also see differences in the input XML constructed by the > AminoAcidSequence object, such as missing articleName='inseq' in > element moby:Simple. > > I've tried this with the Taverna 1.4 release, the stable snapshot from > October 2, and recent builds from cvs (hopefully including the newer > biomoby plug-in module), and it seems I get the same results in all > cases. > > Maybe I'm building the input objects incorrectly? > > Nassib > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > > From edward.kawas at gmail.com Thu Nov 2 15:23:00 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Nov 2006 12:23:00 -0800 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <20061102195731.GA2080@renci.org> Message-ID: <006401c6febc$b22454b0$6900a8c0@notebook> Hi Nassar, It seems that the articlename for the input isnt being set. I will look into this further. Thanks, Eddie > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Nassib Nassar > Sent: Thursday, November 02, 2006 11:58 AM > To: moby-l at lists.open-bio.org > Subject: [MOBY-l] MOBY tutorial - Taverna > > (Thanks to Paul for the test client fix.) > > I'm having trouble using the ConvertAAtoFASTA_AA servlet > example from within Taverna. I made a simple workflow to > test this, and everything works perfectly if I send the > biomoby service a fully formed XML input but not if I build > the input using biomoby processor objects. The workflow runs > both cases in parallel: > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > Inputs: > http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > Error detail: > http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > The error is "Task failed due to problem invoking biomoby service. / > SAXParseException: Premature end of file." Tomcat's log > reports non-XML in the SOAP message (and it actually appears > to be non-ASCII). > I also see differences in the input XML constructed by the > AminoAcidSequence object, such as missing articleName='inseq' > in element moby:Simple. > > I've tried this with the Taverna 1.4 release, the stable > snapshot from October 2, and recent builds from cvs > (hopefully including the newer biomoby plug-in module), and > it seems I get the same results in all cases. > > Maybe I'm building the input objects incorrectly? > > Nassib > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From berend.hoekman at wur.nl Thu Nov 9 07:29:33 2006 From: berend.hoekman at wur.nl (Hoekman, Berend) Date: Thu, 9 Nov 2006 13:29:33 +0100 Subject: [MOBY-l] parsing large XML using java Message-ID: <2E6A821319BCCF4A8FEFDA7E785E0FC705A4CF@scomp0036.wurnet.nl> Hi, I have a problem parsing large xml, using java-moses in axis 1.4, i keep on running agains the: java.lang.OutOfMemoryError: Java heap space; nested exception is: java.lang.OutOfMemoryError: Java heap space error message. When running tomcat 5.0 with 512mb of memory i can send at maximum +-4 mb of xml (i.e. one collection with +- 50.000 objects), and return also 50.000 objects in a collection. This seems a bit odd as this whould imply that the xml is copied 100x when it is parsed. If anyone has some suggesition/ideas how i nevertheless can parse my xml (30 - 50mb), i would like to know. -Berend- From martin.senger at gmail.com Fri Nov 10 04:28:27 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 10 Nov 2006 10:28:27 +0100 Subject: [MOBY-l] parsing large XML using java In-Reply-To: <2E6A821319BCCF4A8FEFDA7E785E0FC705A4CF@scomp0036.wurnet.nl> References: <2E6A821319BCCF4A8FEFDA7E785E0FC705A4CF@scomp0036.wurnet.nl> Message-ID: <4d93f07c0611100128o51a0406ak2b14397b4d6df36e@mail.gmail.com> Hi, I have a problem parsing large xml This can, unfortunately, happen. Unless you design your web services interface in a way that it can accept and send large data in chunks. But BioMoby API is not prepared for it (at least, not yet). Having said that, I have also admit that many times the problem can be diminished (or even removed completely) by looking how various involved software pieces (client, service, etc.) are implemented and improve them. I can look how it can be done better with the jMoby-Moses software. Could you tell me who is reporting the outofmemory error - is it Tomcat? (I guess, it is, reading your email.) The error happens with large data coming to your service, or created by your service? Is it possible to have that large input (or output) that causes the problem so I can play with it here? Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From berend.hoekman at wur.nl Fri Nov 10 08:12:56 2006 From: berend.hoekman at wur.nl (Hoekman, Berend) Date: Fri, 10 Nov 2006 14:12:56 +0100 Subject: [MOBY-l] parsing large XML using java References: <2E6A821319BCCF4A8FEFDA7E785E0FC705A4CF@scomp0036.wurnet.nl> <4d93f07c0611100128o51a0406ak2b14397b4d6df36e@mail.gmail.com> Message-ID: <2E6A821319BCCF4A8FEFDA7E785E0FC705A4D5@scomp0036.wurnet.nl> Hi M. Senger, The problem occurs before my service can start parsing the input, in the processIt method. When debugging i get the impression that the error is caused by tomcat or axis. This because when I send the xml to an empty service (non-moses/biomoby), I get the same memory error. Chunking has been considerd but the xml stucture is in such a format that this is impossible. -The main reason is that multiple collections have to be compared and be merged at the correct position. -(this refers to other xml then the one in: "simpleXMLWhichCausesOutOfMemoryError.txt") I included two files -the example xml which causes the outOfMemoryMessage. (it is plain simple and could be chunked but it purpose was only to determine what the xml-limit of the java-moses services is.) -the java file which supposably does't parse the input (and is probably therefore not related to the problem). (the service accepts a collection of moby objects, did not specify any namespaces) If anything more is needed, please let me know. Thanks for looking into this matter, Berend -----Original Message----- From: Martin Senger [mailto:martin.senger at gmail.com] Sent: Fri 11/10/2006 10:28 AM To: Hoekman, Berend Cc: moby-l at lists.open-bio.org Subject: Re: [MOBY-l] parsing large XML using java Hi, I have a problem parsing large xml This can, unfortunately, happen. Unless you design your web services interface in a way that it can accept and send large data in chunks. But BioMoby API is not prepared for it (at least, not yet). Having said that, I have also admit that many times the problem can be diminished (or even removed completely) by looking how various involved software pieces (client, service, etc.) are implemented and improve them. I can look how it can be done better with the jMoby-Moses software. Could you tell me who is reporting the outofmemory error - is it Tomcat? (I guess, it is, reading your email.) The error happens with large data coming to your service, or created by your service? Is it possible to have that large input (or output) that causes the problem so I can play with it here? Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: simpleXMLWhichCausesOutOfMemoryError.txt Url: http://lists.open-bio.org/pipermail/moby-l/attachments/20061110/f65dff59/attachment-0001.txt From nassar at renci.org Wed Nov 15 16:24:58 2006 From: nassar at renci.org (Nassib Nassar) Date: Wed, 15 Nov 2006 16:24:58 -0500 Subject: [MOBY-l] Source code archive Message-ID: <20061115212458.GA3168@renci.org> Thanks very much for all of your help so far. We're having pretty good luck now in running Biomoby services. We would like to replicate many existing Biomoby services here locally, because our workflows hit them extremely hard. Are any of the service wrappers (source code) publicly available, so that we can avoid recreating them (e.g. blast)? Also, if developers of these wrappers are willing to share them, is there a place where contributed code like this could be archived? Nassib From simont at hmgc.mcw.edu Thu Nov 16 15:22:06 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Thu, 16 Nov 2006 14:22:06 -0600 Subject: [MOBY-l] Ruby & MOBY Message-ID: <66E52884-1FFD-43FE-9BA0-C045FE5A95CA@hmgc.mcw.edu> Is anyone doing any ruby with MOBY services? I saw a thread a while back that referred to a ruby API but google and other searches didnt throw any more light on the subject. I tried a simple test the other day using bog standard ruby approaches to point to a moby service WSDL but got an error at the WSDL parsing stage. Here's what I tried: moby_test.rb require 'soap/wsdlDriver' wsdl = 'http://bioinfo.icapture.ubc.ca:8090/mobyservices/services/ convertKeggGeneId2ProtId?wsdl' driver = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver >ruby moby_test.rb RuntimeError: part: data cannot be resolved method rpcdefinedtype in methodDefCreator.rb at line 144 method collect_rpcparameter in methodDefCreator.rb at line 49 method collect_rpcparameter in methodDefCreator.rb at line 47 method create_param_def in wsdlDriver.rb at line 130 method add_operation in wsdlDriver.rb at line 101 method each in namedelements.rb at line 58 method each in namedelements.rb at line 57 method add_operation in wsdlDriver.rb at line 96 method create_rpc_driver in wsdlDriver.rb at line 40 at top level in moby_test_service.rb at line 6 Program exited. To my eye the WSDL coming from the URL looks reasonable so Im not quite sure what is going wrong here. I've had this code work very nicely with non-moby services (see below) so I was hoping to be able to make my ruby connection to the mobysphere in a similar fashion. Can anyone who is more ruby or MOBY-WSDL savvy suggest what might be amiss? Cheers! Simon. ----- Working service call (non-moby) require 'soap/wsdlDriver' wsdl = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl' driver = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver puts driver.getSupportedDBs() this returns: embl emblsva emblcon emblanncon emblcds medline pdb refseq refseqp hgbase interpro uniprot uniparc uniref100 uniref90 uniref50 jpo_prt epo_prt uspto_prt ipi -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From markw at illuminae.com Thu Nov 16 16:36:45 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 16 Nov 2006 13:36:45 -0800 Subject: [MOBY-l] Ruby & MOBY In-Reply-To: <66E52884-1FFD-43FE-9BA0-C045FE5A95CA@hmgc.mcw.edu> References: <66E52884-1FFD-43FE-9BA0-C045FE5A95CA@hmgc.mcw.edu> Message-ID: I believe that xsd:anyType is an element in the 2001 version of XML Schema, while it used to be xsd:ur-type in earlier versions. It may be that Ruby is expecting the old designation? Perhaps try changing that property to xsd:ur-type and see if it chokes on that... it would be interesting to know! M On Thu, 16 Nov 2006 12:22:06 -0800, Twigger Simon wrote: > >ruby moby_test.rb > RuntimeError: part: data cannot be resolved -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From simont at hmgc.mcw.edu Thu Nov 16 17:43:46 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Thu, 16 Nov 2006 16:43:46 -0600 Subject: [MOBY-l] Ruby & MOBY In-Reply-To: References: <66E52884-1FFD-43FE-9BA0-C045FE5A95CA@hmgc.mcw.edu> Message-ID: <6CCDF779-2B0E-4621-80C9-F68EC20E924E@hmgc.mcw.edu> That would have been nice, wouldn't it... I had tried replacing the various types with values from other working wsdl docs, just to see if I could get past that step but it didnt help. I tried your suggestion but same result. A quick google seems to throw a few instances where ruby is having problems parsing valid wsdl so I'll try and explore some more. Simon. -- On Nov 16, 2006, at 3:36 PM, Mark Wilkinson wrote: > I believe that xsd:anyType is an element in the 2001 version of XML > Schema, while it used to be xsd:ur-type in earlier versions. It > may be that Ruby is expecting the old designation? > > Perhaps try changing that property to xsd:ur-type and see if it > chokes on that... it would be interesting to know! > > M > > > > On Thu, 16 Nov 2006 12:22:06 -0800, Twigger Simon > wrote: > >> >ruby moby_test.rb >> RuntimeError: part: data cannot be resolved > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital From gordonp at ucalgary.ca Tue Nov 21 14:17:22 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 21 Nov 2006 12:17:22 -0700 Subject: [MOBY-l] MOBY tutorial - Taverna In-Reply-To: <20061102195731.GA2080@renci.org> References: <20061102195731.GA2080@renci.org> Message-ID: <456350C2.7010304@ucalgary.ca> Hi all, I finally found some time to look at this Taverna/MobyServlet incompatability. It seems that Taverna does not include an XML declaration () at the start of the MOBY payload. Because the payload did not have this, MobyServlet tried as a last ditch effort to Base64 decode the contents (some old servers sent data this way). That's why you got garbage. Now, between not finding the XML declaration and attempting a base64 decoding, I've inserted a check for the MOBY root tag. Now Taverna jobs work, and will produce the following message in the catalina log: Warning: The MOBY contents was missing an XML declaration, but it is required by the MOBY API, and may stop working in the future without it. Please contact the client's provider to correct this. Perhaps I am wrong, but the MOBY API specifically says that this declaration is required, no? That's why we have to string-encode or base64 encode, etc. the SOAP contents (since processing instructions starting with "xml" are not allowed in the contents of an XML document)? If not, I'll get rid of the warning message... With kind regards, Paul P.S. It may take a few hours for the Web site MobyServlet.war to be mirrored, but the one from CVS is updated. > (Thanks to Paul for the test client fix.) > > I'm having trouble using the ConvertAAtoFASTA_AA servlet example from > within Taverna. I made a simple workflow to test this, and everything > works perfectly if I send the biomoby service a fully formed XML input > but not if I build the input using biomoby processor objects. The > workflow runs both cases in parallel: > > Workflow: http://nassar.europa.renci.org/biomoby_aa2fasta.xml > Inputs: http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml > Error detail: http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml > > The error is "Task failed due to problem invoking biomoby service. / > SAXParseException: Premature end of file." Tomcat's log reports > non-XML in the SOAP message (and it actually appears to be non-ASCII). > I also see differences in the input XML constructed by the > AminoAcidSequence object, such as missing articleName='inseq' in > element moby:Simple. > > I've tried this with the Taverna 1.4 release, the stable snapshot from > October 2, and recent builds from cvs (hopefully including the newer > biomoby plug-in module), and it seems I get the same results in all > cases. > > Maybe I'm building the input objects incorrectly? > > Nassib > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > > From markw at illuminae.com Tue Nov 21 14:54:13 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 21 Nov 2006 11:54:13 -0800 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <456350C2.7010304@ucalgary.ca> References: <20061102195731.GA2080@renci.org> <456350C2.7010304@ucalgary.ca> Message-ID: <1164138853.8447.3.camel@bioinfo.icapture.ubc.ca> On Tue, 2006-11-21 at 12:17 -0700, Paul Gordon wrote: > Perhaps I am wrong, but the MOBY API specifically says that this > declaration is required, no? That's why we have to string-encode or > base64 encode, etc. the SOAP contents (since processing instructions > starting with "xml" are not allowed in the contents of an XML > document)? If not, I'll get rid of the warning message... > That is correct. It does. M From gordonp at ucalgary.ca Tue Nov 21 15:24:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 21 Nov 2006 13:24:41 -0700 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <1164138853.8447.3.camel@bioinfo.icapture.ubc.ca> References: <20061102195731.GA2080@renci.org> <456350C2.7010304@ucalgary.ca> <1164138853.8447.3.camel@bioinfo.icapture.ubc.ca> Message-ID: <45636089.8050802@ucalgary.ca> In that case, I think Taverna (or the BioMOBY plugin?) needs a little tinkering. I'm not sure if it always omits the XML declaration on submission, but is certainly seems to if I load my own sample XML input (which does have the declaration). > On Tue, 2006-11-21 at 12:17 -0700, Paul Gordon wrote: > > >> Perhaps I am wrong, but the MOBY API specifically says that this >> declaration is required, no? That's why we have to string-encode or >> base64 encode, etc. the SOAP contents (since processing instructions >> starting with "xml" are not allowed in the contents of an XML >> document)? If not, I'll get rid of the warning message... >> >> > > > That is correct. It does. > > M > > > > From gordonp at ucalgary.ca Tue Nov 21 15:43:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 21 Nov 2006 13:43:41 -0700 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <009301c70dac$3c9c4a00$6600a8c0@notebook> References: <009301c70dac$3c9c4a00$6600a8c0@notebook> Message-ID: <456364FD.8090508@ucalgary.ca> Good old System.println() on the servlet side :-) Printing request <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> <moby:mobyContent> <moby:mobyData moby:queryID="1"> <moby:Simple moby:articleName="inseq"> <AminoAcidSequence xmlns="http://www.biomoby.org/moby" namespace="NCBI_gi" id="15898917" articleName=""> <String namespace="" id="" articleName="SequenceString">MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNAIVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGEIKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSSDIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLLTTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAFVGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDGGGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIPSINKEERERRYNAWKEAVKRSLGWEKSLGSK</String> <Integer namespace="" id="" articleName="Length">499</Integer> </AminoAcidSequence> </moby:Simple> </moby:mobyData> </moby:mobyContent> </moby:MOBY> > Hi Paul, > > The plugin should be outputting the xml declaration. How did you determine that > it wasn't? > > Thanks, > > Eddie > > >> -----Original Message----- >> From: moby-l-bounces at lists.open-bio.org >> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Paul Gordon >> Sent: Tuesday, November 21, 2006 12:25 PM >> To: markw at illuminae.com >> Cc: moby-l at lists.open-bio.org >> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna >> >> In that case, I think Taverna (or the BioMOBY plugin?) needs >> a little tinkering. I'm not sure if it always omits the XML >> declaration on submission, but is certainly seems to if I >> load my own sample XML input (which does have the declaration). >> >>> On Tue, 2006-11-21 at 12:17 -0700, Paul Gordon wrote: >>> >>> >>> >>>> Perhaps I am wrong, but the MOBY API specifically says that this >>>> declaration is required, no? That's why we have to >>>> >> string-encode or >> >>>> base64 encode, etc. the SOAP contents (since processing >>>> >> instructions >> >>>> starting with "xml" are not allowed in the contents of an XML >>>> document)? If not, I'll get rid of the warning message... >>>> >>>> >>>> >>> That is correct. It does. >>> >>> M >>> >>> >>> >>> >>> >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> > > > From edward.kawas at gmail.com Tue Nov 21 15:46:34 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 21 Nov 2006 12:46:34 -0800 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <456364FD.8090508@ucalgary.ca> Message-ID: <009701c70dae$23922780$6600a8c0@notebook> Sorry, but the declaration that you are talking about (the one missing) is the one inside the soap message? Eddie > -----Original Message----- > From: Paul Gordon [mailto:gordonp at ucalgary.ca] > Sent: Tuesday, November 21, 2006 12:44 PM > To: Edward Kawas > Cc: moby-l at lists.open-bio.org; Mark Wilkinson > Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna > > Good old System.println() on the servlet side :-) > > Printing request > xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" > > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > > > soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encodin > g/" > xmlns:ns1="http://biomoby.org/" > > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > ><moby:MOBY > xmlns:moby="http://www.biomoby.org/moby"> > > ; > <moby:mobyContent> > <moby:mobyData moby:queryID="1"> > <moby:Simple moby:articleName="inseq"> > <AminoAcidSequence > xmlns="http://www.biomoby.org/moby" > ; > namespace="NCBI_gi" id="15898917" > articleName=""> > <String namespace="" id="" > articleName="SequenceString">MPGGFILAIDEGTTSARAII YNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNA IVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGE> IKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSS > DIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLL > TTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAF > VGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDG > GGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIP > SINKEERERRYNAWKEAVKRSLGWEKSLGSK</String> > <Integer namespace="" id="" > articleName="Length">499</Integer> > </AminoAcidSequence> > </moby:Simple> > </moby:mobyData> > </moby:mobyContent> > </moby:MOBY> nv:Body> > > > > Hi Paul, > > The plugin should be outputting the xml declaration. > How did you determine that > it wasn't? > > Thanks, > > Eddie > > > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On > Behalf Of Paul Gordon > Sent: Tuesday, November 21, 2006 12:25 PM > To: markw at illuminae.com > Cc: moby-l at lists.open-bio.org > Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna > > In that case, I think Taverna (or the BioMOBY > plugin?) needs > a little tinkering. I'm not sure if it always > omits the XML > declaration on submission, but is certainly > seems to if I > load my own sample XML input (which does have > the declaration). > > > On Tue, 2006-11-21 at 12:17 -0700, Paul > Gordon wrote: > > > > > Perhaps I am wrong, but the > MOBY API specifically says that this > declaration is required, no? > That's why we have to > > > string-encode or > > > base64 encode, etc. the SOAP > contents (since processing > > > instructions > > > starting with "xml" are not > allowed in the contents of an XML > document)? If not, I'll get > rid of the warning message... > > > > > > That is correct. It does. > > M > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > > > > > > > From edward.kawas at gmail.com Tue Nov 21 15:58:40 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 21 Nov 2006 12:58:40 -0800 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <456366AB.3070509@ucalgary.ca> Message-ID: <009b01c70daf$d445f1a0$6600a8c0@notebook> Hmm, I will look into it, but when I actually call the webservice, I use an XML string that is created by http://www.jdom.org/docs/apidocs/org/jdom/output/Format.html#getPrettyFormat() and the method states that it includes the declaration. Eddie > -----Original Message----- > From: Paul Gordon [mailto:gordonp at ucalgary.ca] > Sent: Tuesday, November 21, 2006 12:51 PM > To: Edward Kawas > Cc: moby-l at lists.open-bio.org; 'Mark Wilkinson' > Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna > > The missing bit is the XML declaration for the MOBY payload, > not the one for the SOAP envelope. > > So, the message should look like: > > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > ><?xml > version="1.0"><moby:MOBY > > instead of the current: > > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > ><moby:MOBY > > > Sorry, but the declaration that you are talking about > (the one missing) is the > one inside the soap message? > > Eddie > > > > -----Original Message----- > From: Paul Gordon [mailto:gordonp at ucalgary.ca] > Sent: Tuesday, November 21, 2006 12:44 PM > To: Edward Kawas > Cc: moby-l at lists.open-bio.org; Mark Wilkinson > Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna > > Good old System.println() on the servlet side :-) > > Printing request > > xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" > > > > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > > > > > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > > > > > > > > > soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encodin > g/" > > > xmlns:ns1="http://biomoby.org/" > > > > > > > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > > > ><moby:MOBY > > xmlns:moby="http://www.biomoby.org/moby"> > > > > ; > <moby:mobyContent> > <moby:mobyData moby:queryID="1"> > <moby:Simple > moby:articleName="inseq"> > <AminoAcidSequence > xmlns="http://www.biomoby.org/moby" > > ; > namespace="NCBI_gi" id="15898917" > articleName=""> > <String namespace="" > id="" > > articleName="SequenceString">MPGGFILAIDEGTTSARAII > > > > YNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQ > RETTILWDAISGKPIYNA > IVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGE> > IKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSS > > > > DIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLL > > TTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAF > > VGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDG > > GGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIP > SINKEERERRYNAWKEAVKRSLGWEKSLGSK</String> > <Integer namespace="" > id="" > articleName="Length">499</Integer> > </AminoAcidSequence> > </moby:Simple> > </moby:mobyData> > </moby:mobyContent> > > </moby:MOBY> nv:Body> > > > > Hi Paul, > > The plugin should be outputting the xml > declaration. > How did you determine that > it wasn't? > > Thanks, > > Eddie > > > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > > [mailto:moby-l-bounces at lists.open-bio.org] On > Behalf Of Paul Gordon > Sent: Tuesday, November 21, > 2006 12:25 PM > To: markw at illuminae.com > Cc: moby-l at lists.open-bio.org > Subject: Re: [MOBY-l] [moby] > Re: MOBY tutorial - Taverna > > In that case, I think Taverna > (or the BioMOBY > plugin?) needs > a little tinkering. I'm not > sure if it always > omits the XML > declaration on submission, but > is certainly > seems to if I > load my own sample XML input > (which does have > the declaration). > > > On Tue, 2006-11-21 at > 12:17 -0700, Paul > Gordon wrote: > > > > > Perhaps I am > wrong, but the > MOBY API specifically says that this > declaration is > required, no? > That's why we have to > > > string-encode or > > > base64 encode, > etc. the SOAP > contents (since processing > > > instructions > > > starting with > "xml" are not > allowed in the contents of an XML > document)? If > not, I'll get > rid of the warning message... > > > > > > That is correct. It does. > > M > > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-l > > > > > > > > > > > > > > > > From gordonp at ucalgary.ca Tue Nov 21 15:51:42 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 21 Nov 2006 13:51:42 -0700 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <456366AB.3070509@ucalgary.ca> References: <009701c70dae$23922780$6600a8c0@notebook> <456366AB.3070509@ucalgary.ca> Message-ID: <456366DE.1030603@ucalgary.ca> Oops, missed a semi-colon: <?xml version="1.0"><moby:MOBY From gordonp at ucalgary.ca Tue Nov 21 15:50:51 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 21 Nov 2006 13:50:51 -0700 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <009701c70dae$23922780$6600a8c0@notebook> References: <009701c70dae$23922780$6600a8c0@notebook> Message-ID: <456366AB.3070509@ucalgary.ca> The missing bit is the XML declaration for the MOBY payload, not the one for the SOAP envelope. So, the message should look like: <?xml version="1.0"><moby:MOBY instead of the current: <moby:MOBY > Sorry, but the declaration that you are talking about (the one missing) is the > one inside the soap message? > > Eddie > > >> -----Original Message----- >> From: Paul Gordon [mailto:gordonp at ucalgary.ca] >> Sent: Tuesday, November 21, 2006 12:44 PM >> To: Edward Kawas >> Cc: moby-l at lists.open-bio.org; Mark Wilkinson >> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna >> >> Good old System.println() on the servlet side :-) >> >> Printing request >> > xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" >> >> xmlns:xsd="http://www.w3.org/2001/XMLSchema" >> >> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >> >> >>> >> >> soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encodin >> g/" >> xmlns:ns1="http://biomoby.org/" >> >>> >> >> xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" >> ><moby:MOBY >> xmlns:moby="http://www.biomoby.org/moby"> >> > ; >> <moby:mobyContent> >> <moby:mobyData moby:queryID="1"> >> <moby:Simple moby:articleName="inseq"> >> <AminoAcidSequence >> xmlns="http://www.biomoby.org/moby" >> ; >> namespace="NCBI_gi" id="15898917" >> articleName=""> >> <String namespace="" id="" >> articleName="SequenceString">MPGGFILAIDEGTTSARAII >> > YNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNA > IVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGE> > IKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSS > >> DIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLL >> TTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAF >> VGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDG >> GGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIP >> SINKEERERRYNAWKEAVKRSLGWEKSLGSK</String> >> <Integer namespace="" id="" >> articleName="Length">499</Integer> >> </AminoAcidSequence> >> </moby:Simple> >> </moby:mobyData> >> </moby:mobyContent> >> </moby:MOBY>> nv:Body> >> >> >> >> Hi Paul, >> >> The plugin should be outputting the xml declaration. >> How did you determine that >> it wasn't? >> >> Thanks, >> >> Eddie >> >> >> >> -----Original Message----- >> From: moby-l-bounces at lists.open-bio.org >> [mailto:moby-l-bounces at lists.open-bio.org] On >> Behalf Of Paul Gordon >> Sent: Tuesday, November 21, 2006 12:25 PM >> To: markw at illuminae.com >> Cc: moby-l at lists.open-bio.org >> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna >> >> In that case, I think Taverna (or the BioMOBY >> plugin?) needs >> a little tinkering. I'm not sure if it always >> omits the XML >> declaration on submission, but is certainly >> seems to if I >> load my own sample XML input (which does have >> the declaration). >> >> >> On Tue, 2006-11-21 at 12:17 -0700, Paul >> Gordon wrote: >> >> >> >> >> Perhaps I am wrong, but the >> MOBY API specifically says that this >> declaration is required, no? >> That's why we have to >> >> >> string-encode or >> >> >> base64 encode, etc. the SOAP >> contents (since processing >> >> >> instructions >> >> >> starting with "xml" are not >> allowed in the contents of an XML >> document)? If not, I'll get >> rid of the warning message... >> >> >> >> >> >> That is correct. It does. >> >> M >> >> >> >> >> >> >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> >> >> >> >> >> >> >> >> > > > From MCCon012 at mc.duke.edu Tue Nov 21 16:04:32 2006 From: MCCon012 at mc.duke.edu (Patrick McConnell) Date: Tue, 21 Nov 2006 16:04:32 -0500 Subject: [MOBY-l] Patrick McConnell is out of the office 11/17-11/29 Message-ID: I will be out of the office starting 11/17/2006 and will not return until 11/29/2006. Dear colleague, I apologize if you receive this email more than once. I wanted to let you know that I will be out of the office starting Friday, November 17th and will not return until Wednesday, November 29th. I will not be reachable by phone or email during this time because I will be on vacation in India. Please contact the following people if you have a question about a specific project: caGrid reference implementation: Scott Oster (oster at bmi.osu.edu) caTRIP: Ram Chilukuri (ram.chilukuri at semanticbits.com) C3PR: Ram Chilukuri (ram.chilukuri at semanticbits.com) RProteomics: Salvatore Mungal (salvatore.mungal at duke.edu) caGrid Adoption: Salvatore Mungal (salvatore.mungal at duke.edu) caBIG Architecture: Pankaj Agarwal (p.agarwal at duke.edu) caBIG VCDE: Salvatore Mungal (salvatore.mungal at duke.edu) caBIG ICR: Salvatore Mungal (salvatore.mungal at duke.edu) Songbird cDNA library: Pankaj Agarwal (p.agarwal at duke.edu) CAMDA: Emily Allred (emily.allred at duke.edu) For anything else, please contact Emily Allred (emily.allred at duke.edu). Sincerely, -Patrick McConnell Duke Bioinformatics Shared Resource Duke Comprehensive Cancer Center patrick.mcconnell at duke.edu From edward.kawas at gmail.com Tue Nov 21 15:32:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 21 Nov 2006 12:32:57 -0800 Subject: [MOBY-l] [moby] Re: MOBY tutorial - Taverna In-Reply-To: <45636089.8050802@ucalgary.ca> Message-ID: <009301c70dac$3c9c4a00$6600a8c0@notebook> Hi Paul, The plugin should be outputting the xml declaration. How did you determine that it wasn't? Thanks, Eddie > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Tuesday, November 21, 2006 12:25 PM > To: markw at illuminae.com > Cc: moby-l at lists.open-bio.org > Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna > > In that case, I think Taverna (or the BioMOBY plugin?) needs > a little tinkering. I'm not sure if it always omits the XML > declaration on submission, but is certainly seems to if I > load my own sample XML input (which does have the declaration). > > On Tue, 2006-11-21 at 12:17 -0700, Paul Gordon wrote: > > > > > >> Perhaps I am wrong, but the MOBY API specifically says that this > >> declaration is required, no? That's why we have to > string-encode or > >> base64 encode, etc. the SOAP contents (since processing > instructions > >> starting with "xml" are not allowed in the contents of an XML > >> document)? If not, I'll get rid of the warning message... > >> > >> > > > > > > That is correct. It does. > > > > M > > > > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Thu Nov 30 13:54:14 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 30 Nov 2006 10:54:14 -0800 Subject: [MOBY-l] Taverna-MOBY manuscript published Message-ID: BioMoby extensions to the Taverna workflow management and enactment software Edward A Kawas , Martin Senger and Mark D Wilkinson BMC Bioinformatics 2006, 7:523 doi:10.1186/1471-2105-7-523 http://www.biomedcentral.com/1471-2105/7/523/abstract Cheers all! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From carole.goble at manchester.ac.uk Thu Nov 30 14:01:04 2006 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Thu, 30 Nov 2006 19:01:04 +0000 Subject: [MOBY-l] Taverna-MOBY manuscript published In-Reply-To: References: Message-ID: <456F2A70.8060805@manchester.ac.uk> Mark hurrah! Carole > BioMoby extensions to the Taverna workflow management and enactment > software > Edward A Kawas , Martin Senger and Mark D Wilkinson > BMC Bioinformatics 2006, 7:523 doi:10.1186/1471-2105-7-523 > > http://www.biomedcentral.com/1471-2105/7/523/abstract > > Cheers all! > > M > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital